Difference between revisions of "WS230 Models.wrm"
From WormBaseWiki
Jump to navigationJump to search| Line 50: | Line 50: | ||
| − | + | Ace2SO class: gives a mapping from Acedb objects to their SO terms. | |
| − | + | ||
| − | + | SO_subpart_tags - Tag pointing to subpart of this object, e.g. "Source_exon". | |
| − | + | SO_parent_obj_tag - Tag pointing to semantic parent of this object, e.g. "Gene" | |
| − | + | SO_children - this object has child objects which refer to it. | |
?Ace2SO Description UNIQUE Text | ?Ace2SO Description UNIQUE Text | ||
| Line 111: | Line 111: | ||
------ | ------ | ||
| − | + | Addition | |
GFF_SO UNIQUE ?SO_term UNIQUE ?Ace2SO | GFF_SO UNIQUE ?SO_term UNIQUE ?Ace2SO | ||
Revision as of 10:11, 1 February 2012
Contents
Models Tagged for WS230
This cycle we see introduction of models to supplement the new gff3 dumping functionality being added to the acedb code.
Model Changes
Old ?SO_term Term ?Text
New ?SO_term SO_name ?Text
SO_definition ?Text
SO_synonym ?Text
SO_version ?Text
New
Sequence_alteration
Old
Sequence_variant Synonym ?Text Definition ?Text
New
Derived_from ?SO_term XREF Derives
Member_of ?SO_term XREF Member
Old
Derived_from ?SO_term XREF Derived
New
Derives ?SO_term XREF Derived_from
Member ?SO_term XREF Member_of
Old
Derived ?SO_term XREF Derived_from
Attributes_of Feature ?Feature XREF SO_term
Ace2SO class: gives a mapping from Acedb objects to their SO terms.
SO_subpart_tags - Tag pointing to subpart of this object, e.g. "Source_exon". SO_parent_obj_tag - Tag pointing to semantic parent of this object, e.g. "Gene" SO_children - this object has child objects which refer to it.
?Ace2SO Description UNIQUE Text
SO_subparts Exons UNIQUE ?SO_Term
Introns UNIQUE ?SO_term
Coding_region UNIQUE ?SO_term
No_span
SO_parent_obj_tag UNIQUE Text
SO_children
---
Version SOFA_ontology UNIQUE Float // Analogous to GO, the SO version number is only to be attached
SOFA_definition UNIQUE Float // to three parent SOFA terms under Located_sequence_feature
New
Oligo ?Oligo XREF In_sequence Int UNIQUE Int ?Method
Old
Oligo ?Oligo XREF In_sequence Int UNIQUE Int // for OSP and human mapping mostly
New
Match_string UNIQUE RefFwd_HitFwd UNIQUE Text
RefFwd_HitRev UNIQUE Text
RefRev_HitFwd UNIQUE Text
RefRev_HitRev UNIQUE Text
Align_id Text
Target_species UNIQUE ?Species
EMBL_dump UNIQUE EMBL_dump_YES
EMBL_dump_NO
// overrides for embl dump based on method
EMBL_qualifier Text// additional to those in the method, includes '/'
Old
Target_species UNIQUE ?Species
EMBL_dump UNIQUE EMBL_dump_YES
EMBL_dump_NO
// overrides for embl dump based on method
EMBL_qualifier Text
// additional to those in the method, includes '/'
New
SO_term ?SO_term
Old
SO_term ?SO_term XREF Feature
Addition
GFF_SO UNIQUE ?SO_term UNIQUE ?Ace2SO
